Genomic prediction for growth using a low-density SNP panel in dromedary camels

Abstract For thousands of years, camels have produced meat, milk, and fiber in harsh desert conditions. For a sustainable development to provide protein resources from desert areas, it is necessary to pay attention to genetic improvement in camel breeding. By using genotyping-by-sequencing (GBS) met...

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Autores principales:	Morteza Bitaraf Sani, Javad Zare Harofte, Mohammad Hossein Banabazi, Saeid Esmaeilkhanian, Ali Shafei Naderi, Nader Salim, Abbas Teimoori, Ahmad Bitaraf, Mohammad Zadehrahmani, Pamela Anna Burger, Vincenzo Landi, Mohammad Silawi, Afsaneh Taghipour Sheshdeh, Mohammad Ali Faghihi
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/ed43fc635fa14977ba830e7f57fb8282
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spelling	oai:doaj.org-article:ed43fc635fa14977ba830e7f57fb82822021-12-02T14:37:29ZGenomic prediction for growth using a low-density SNP panel in dromedary camels10.1038/s41598-021-87296-72045-2322https://doaj.org/article/ed43fc635fa14977ba830e7f57fb82822021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-87296-7https://doaj.org/toc/2045-2322Abstract For thousands of years, camels have produced meat, milk, and fiber in harsh desert conditions. For a sustainable development to provide protein resources from desert areas, it is necessary to pay attention to genetic improvement in camel breeding. By using genotyping-by-sequencing (GBS) method we produced over 14,500 genome wide markers to conduct a genome- wide association study (GWAS) for investigating the birth weight, daily gain, and body weight of 96 dromedaries in the Iranian central desert. A total of 99 SNPs were associated with birth weight, daily gain, and body weight (p-value < 0.002). Genomic breeding values (GEBVs) were estimated with the BGLR package using (i) all 14,522 SNPs and (ii) the 99 SNPs by GWAS. Twenty-eight SNPs were associated with birth weight, daily gain, and body weight (p-value < 0.001). Annotation of the genomic region (s) within ± 100 kb of the associated SNPs facilitated prediction of 36 candidate genes. The accuracy of GEBVs was more than 0.65 based on all 14,522 SNPs, but the regression coefficients for birth weight, daily gain, and body weight were 0.39, 0.20, and 0.23, respectively. Because of low sample size, the GEBVs were predicted using the associated SNPs from GWAS. The accuracy of GEBVs based on the 99 associated SNPs was 0.62, 0.82, and 0.57 for birth weight, daily gain, and body weight. This report is the first GWAS using GBS on dromedary camels and identifies markers associated with growth traits that could help to plan breeding program to genetic improvement. Further researches using larger sample size and collaboration of the camel farmers and more profound understanding will permit verification of the associated SNPs identified in this project. The preliminary results of study show that genomic selection could be the appropriate way to genetic improvement of body weight in dromedary camels, which is challenging due to a long generation interval, seasonal reproduction, and lack of records and pedigrees.Morteza Bitaraf SaniJavad Zare HarofteMohammad Hossein BanabaziSaeid EsmaeilkhanianAli Shafei NaderiNader SalimAbbas TeimooriAhmad BitarafMohammad ZadehrahmaniPamela Anna BurgerVincenzo LandiMohammad SilawiAfsaneh Taghipour SheshdehMohammad Ali FaghihiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Morteza Bitaraf Sani Javad Zare Harofte Mohammad Hossein Banabazi Saeid Esmaeilkhanian Ali Shafei Naderi Nader Salim Abbas Teimoori Ahmad Bitaraf Mohammad Zadehrahmani Pamela Anna Burger Vincenzo Landi Mohammad Silawi Afsaneh Taghipour Sheshdeh Mohammad Ali Faghihi Genomic prediction for growth using a low-density SNP panel in dromedary camels
description	Abstract For thousands of years, camels have produced meat, milk, and fiber in harsh desert conditions. For a sustainable development to provide protein resources from desert areas, it is necessary to pay attention to genetic improvement in camel breeding. By using genotyping-by-sequencing (GBS) method we produced over 14,500 genome wide markers to conduct a genome- wide association study (GWAS) for investigating the birth weight, daily gain, and body weight of 96 dromedaries in the Iranian central desert. A total of 99 SNPs were associated with birth weight, daily gain, and body weight (p-value < 0.002). Genomic breeding values (GEBVs) were estimated with the BGLR package using (i) all 14,522 SNPs and (ii) the 99 SNPs by GWAS. Twenty-eight SNPs were associated with birth weight, daily gain, and body weight (p-value < 0.001). Annotation of the genomic region (s) within ± 100 kb of the associated SNPs facilitated prediction of 36 candidate genes. The accuracy of GEBVs was more than 0.65 based on all 14,522 SNPs, but the regression coefficients for birth weight, daily gain, and body weight were 0.39, 0.20, and 0.23, respectively. Because of low sample size, the GEBVs were predicted using the associated SNPs from GWAS. The accuracy of GEBVs based on the 99 associated SNPs was 0.62, 0.82, and 0.57 for birth weight, daily gain, and body weight. This report is the first GWAS using GBS on dromedary camels and identifies markers associated with growth traits that could help to plan breeding program to genetic improvement. Further researches using larger sample size and collaboration of the camel farmers and more profound understanding will permit verification of the associated SNPs identified in this project. The preliminary results of study show that genomic selection could be the appropriate way to genetic improvement of body weight in dromedary camels, which is challenging due to a long generation interval, seasonal reproduction, and lack of records and pedigrees.
format	article
author	Morteza Bitaraf Sani Javad Zare Harofte Mohammad Hossein Banabazi Saeid Esmaeilkhanian Ali Shafei Naderi Nader Salim Abbas Teimoori Ahmad Bitaraf Mohammad Zadehrahmani Pamela Anna Burger Vincenzo Landi Mohammad Silawi Afsaneh Taghipour Sheshdeh Mohammad Ali Faghihi
author_facet	Morteza Bitaraf Sani Javad Zare Harofte Mohammad Hossein Banabazi Saeid Esmaeilkhanian Ali Shafei Naderi Nader Salim Abbas Teimoori Ahmad Bitaraf Mohammad Zadehrahmani Pamela Anna Burger Vincenzo Landi Mohammad Silawi Afsaneh Taghipour Sheshdeh Mohammad Ali Faghihi
author_sort	Morteza Bitaraf Sani
title	Genomic prediction for growth using a low-density SNP panel in dromedary camels
title_short	Genomic prediction for growth using a low-density SNP panel in dromedary camels
title_full	Genomic prediction for growth using a low-density SNP panel in dromedary camels
title_fullStr	Genomic prediction for growth using a low-density SNP panel in dromedary camels
title_full_unstemmed	Genomic prediction for growth using a low-density SNP panel in dromedary camels
title_sort	genomic prediction for growth using a low-density snp panel in dromedary camels
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/ed43fc635fa14977ba830e7f57fb8282
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Genomic prediction for growth using a low-density SNP panel in dromedary camels

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